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		<title>About MZmine 2 - Usage and workflow</title>
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<h1>Usage and workflow</h1>

<h2>Starting MZmine 2</h2>

<p>
MZmine 2 can run on any platform which has a Java runtime available (version 1.6 or higher). 
A startup script is provided for MS Windows (startMZmine_Windows.bat), Mac OS X (startMZmine_MacOSX.command) and Linux (startMZmine_Linux.sh) environments.
The startup script may be edited to tweak various Java runtime parameters:
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<dl>
  <dt>HEAP_SIZE</dt>
  <dd>The amount of memory allocated for the Java Virtual Machine.
   Default value is set to 1GB. 
   If your computer has more RAM available and you wish to use it for MZmine 2, please change this value.
  </dd>
  <dt>NIST_MS_SEARCH_PATH</dt>
  <dd>The path to NIST database installation (optional, only on Windows)</dd>
  <dt>R_HOME</dt>
  <dd>The path to R installation (optional)</dd>
</dl>


<h2>MZmine 2 desktop</h2>

<p>
The following screenshot describes the main components of the MZmine 2 desktop:
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<p>
<img src="mainWindow.png">
</p>


<h2>Data processing workflow</h2>

<p>
A typical workflow for processing mass spectrometry data using MZmine 2 consists of the following steps (note that many of these steps are optional and may be skipped):
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<p>
<ol>
<li><a href="/net/sf/mzmine/modules/rawdatamethods/rawdataimport/help/help.html">Raw data import</a></li>
<li>Generation of mass lists (detected ions) for each scan using the <a href="/net/sf/mzmine/modules/rawdatamethods/peakpicking/massdetection/help/help.html">Mass detector</a></li>
<li>(Optional) Mass list filtering for <a href="/net/sf/mzmine/modules/masslistmethods/shoulderpeaksfilter/help/help.html">FTMS shoulder peaks</a></li>

<li>Detection of chromatograms using the <a href="/net/sf/mzmine/modules/masslistmethods/chromatogrambuilder/help/help.html">Chromatogram builder</a></li>
<li><a href="/net/sf/mzmine/modules/peaklistmethods/peakpicking/deconvolution/help/help.html">Deconvolution</a> of chromatograms into individual peaks</li>
<li>Removing of <a href="/net/sf/mzmine/modules/peaklistmethods/isotopes/deisotoper/help/help.html">isotopes</a></li>
<li>Identification of 
<a href="/net/sf/mzmine/modules/peaklistmethods/identification/fragmentsearch/help/help.html">fragments</a>,
<a href="/net/sf/mzmine/modules/peaklistmethods/identification/adductsearch/help/help.html">adducts</a> and
<a href="/net/sf/mzmine/modules/peaklistmethods/identification/complexsearch/help/help.html">peak complexes</a>,
</li>
<li>Normalization of retention time using the <a href="/net/sf/mzmine/modules/peaklistmethods/normalization/rtnormalizer/help/help.html">Retention time normalizer</a></li>
<li>Alignment using the <a href="/net/sf/mzmine/modules/peaklistmethods/alignment/join/help/help.html">Join aligner</a> or <a href="/net/sf/mzmine/modules/peaklistmethods/alignment/ransac/help/help.html">RANSAC aligner</a></li>
<li>Gap filling using the <a href="/net/sf/mzmine/modules/peaklistmethods/gapfilling/peakfinder/help/help.html">Peak finder</a> or <a href="/net/sf/mzmine/modules/peaklistmethods/gapfilling/samerange/help/help.html">Same range gap filler</a></li>
<li>Normalization using the <a href="/net/sf/mzmine/modules/peaklistmethods/normalization/linear/help/help.html">Linear normalizer</a> or <a href="/net/sf/mzmine/modules/peaklistmethods/normalization/standardcompound/help/help.html">Standard compound normalizer</a></li>
<li>Identification using a <a href="/net/sf/mzmine/modules/peaklistmethods/identification/custom/help/help.html">custom database</a> or <a href="/net/sf/mzmine/modules/peaklistmethods/identification/dbsearch/help/help.html">online databases</a></li>
<li>Data analysis, export, visualization etc..</li>
</ol>
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